BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236084.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,485,988 number of mapped reads = 1,285,751 (86.52%) number of supplementary alignments = 8,030 (0.54%) number of secondary alignments = 0 number of mapped bases = 84,153,202 bp number of sequenced bases = 84,112,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,539 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7025 >>>>>>> ACTG content number of A's = 22,848,736 bp (27.16%) number of C's = 15,072,854 bp (17.92%) number of T's = 27,087,656 bp (32.2%) number of G's = 19,054,844 bp (22.65%) number of N's = 48,704 bp (0.06%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 689,045 number of insertions = 6,152 mapped reads with insertion percentage = 0.47% number of deletions = 23,266 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2674X There is a 2.34% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6069256 0.024350013555232024 0.42135867704061963 chr2 243199373 5489990 0.02257403023814539 0.3075592378914943 chr3 198022430 6428895 0.032465488884264274 0.20269006072264 chr4 191154276 4841290 0.025326611056296747 0.2024717504748513 chr5 180915260 4464758 0.02467872527723753 0.17744179205678987 chr6 171115067 9121193 0.053304441040250415 0.2981732746188073 chr7 159138663 4988740 0.031348384521742524 0.40257219889482265 chr8 146364022 4877417 0.03332387927956776 0.34347306725097665 chr9 141213431 3601728 0.025505562569328125 0.2578675069954277 chr10 135534747 3539980 0.026118615914780877 0.2549495328625841 chr11 135006516 2644804 0.0195901951873197 0.19810810517523783 chr12 133851895 2708245 0.020233146493742207 0.1667961455982634 chr13 115169878 4159788 0.03611871499942025 0.21553950770012484 chr14 107349540 2289556 0.021328046678169277 0.17272876791121203 chr15 102531392 1931026 0.018833510033688022 0.15672084001075307 chr16 90354753 2497213 0.02763787091532418 0.19783574713165972 chr17 81195210 1875237 0.02309541412603034 0.1859125335378899 chr18 78077248 2751483 0.03524052230939287 0.37693627548382935 chr19 59128983 1825109 0.03086657181301427 0.3244366463735818 chr20 63025520 1719838 0.02728796208266112 0.19027701181404497 chr21 48129895 1395863 0.02900199553728509 0.20581139391856834 chr22 51304566 959012 0.018692527288896664 0.15271526854542164 chrMT 16571 43526 2.6266368957817874 2.3776440096072253 chrX 155270560 3732601 0.024039334951841483 0.1876483949197086 chrY 59373566 196654 0.0033121473620095513 0.11072383706240832